1
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Johnson ML, Hay BA, Maselko M. Altering traits and fates of wild populations with Mendelian DNA sequence modifying Allele Sails. Nat Commun 2024; 15:6665. [PMID: 39138152 PMCID: PMC11322531 DOI: 10.1038/s41467-024-50992-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/26/2024] [Indexed: 08/15/2024] Open
Abstract
Population-scale genome modification can alter the composition or fate of wild populations. Synthetic gene drives provide one set of tools, but their use is complicated by scientific, regulatory, and social issues associated with transgene persistence and flow. Here we propose an alternative approach. An Allele Sail consists of a genome editor (the Wind) that introduces DNA sequence edits, and is inherited in a Mendelian fashion. Meanwhile, the edits (the Sail) experience an arithmetic, Super-Mendelian increase in frequency. We model this system and identify contexts in which a single, low frequency release of an editor brings edits to a very high frequency. We also identify conditions in which manipulation of sex determination can bring about population suppression. In regulatory frameworks that distinguish between transgenics (GMO) and their edited non-transgenic progeny (non-GMO) Allele Sails may prove useful since the spread and persistence of the GM component can be limited.
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Affiliation(s)
- Michelle L Johnson
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, MC156-29, Pasadena, CA, 91125, USA
| | - Bruce A Hay
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, MC156-29, Pasadena, CA, 91125, USA.
| | - Maciej Maselko
- Applied BioSciences, Macquarie University, North Ryde, NSW, 2109, Australia.
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2
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Ostalé CM, Prado AD, Martín M, Esteban N, López-Varea A, de Celis JF. A function of spalt major as a sequence-specific DNA binding transcription factor mediates repression of knirps in the Drosophila wing imaginal disc. Dev Biol 2024; 510:40-49. [PMID: 38493946 DOI: 10.1016/j.ydbio.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/30/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
The Spalt transcriptional regulators participate in a variety of cell fate decisions during multicellular development. Vertebrate Spalt proteins have been mostly associated to the organization of heterochromatic regions, but they also contribute regulatory functions through binding to A/T rich motives present in their target genes. The developmental processes in which the Drosophila spalt genes participate are well known through genetic analysis, but the mechanism by which the Spalt proteins regulate transcription are still unknown. Furthermore, despite the prominent changes in gene expression associated to mutations in the spalt genes, the specific DNA sequences they bind are unknow. Here, we analyze a DNA fragment present in the regulatory region of the knirps gene. Spalt proteins are candidate repressors of knirps expression during the formation of the venation pattern in the wing disc, and we identified a minimal conserved 30bp sequence that binds to Spalt major both in vivo and in vitro. This sequence mediates transcriptional repression in the central region of the wing blade, constituting the first confirmed case of a direct regulatory interaction between Spalt major and its target DNA in Drosophila. Interestingly, we also find similar sequences in a set of eight novel candidate Spalt target genes, pointing to a common mechanism of transcriptional repression mediated by Spalt proteins.
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Affiliation(s)
- Cristina M Ostalé
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Alicia Del Prado
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Mercedes Martín
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Nuria Esteban
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Ana López-Varea
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Jose F de Celis
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid, 28049, Spain.
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3
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Auradkar A, Guichard A, Kaduwal S, Sneider M, Bier E. tgCRISPRi: efficient gene knock-down using truncated gRNAs and catalytically active Cas9. Nat Commun 2023; 14:5587. [PMID: 37696787 PMCID: PMC10495392 DOI: 10.1038/s41467-023-40836-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/14/2023] [Indexed: 09/13/2023] Open
Abstract
CRISPR-interference (CRISPRi), a highly effective method for silencing genes in mammalian cells, employs an enzymatically dead form of Cas9 (dCas9) complexed with one or more guide RNAs (gRNAs) with 20 nucleotides (nt) of complementarity to transcription initiation sites of target genes. Such gRNA/dCas9 complexes bind to DNA, impeding transcription of the targeted locus. Here, we present an alternative gene-suppression strategy using active Cas9 complexed with truncated gRNAs (tgRNAs). Cas9/tgRNA complexes bind to specific target sites without triggering DNA cleavage. When targeted near transcriptional start sites, these short 14-15 nts tgRNAs efficiently repress expression of several target genes throughout somatic tissues in Drosophila melanogaster without generating any detectable target site mutations. tgRNAs also can activate target gene expression when complexed with a Cas9-VPR fusion protein or modulate enhancer activity, and can be incorporated into a gene-drive, wherein a traditional gRNA sustains drive while a tgRNA inhibits target gene expression.
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Affiliation(s)
- Ankush Auradkar
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Annabel Guichard
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Saluja Kaduwal
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Marketta Sneider
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA.
- Tata Institute for Genetics and Society - UCSD, La Jolla, USA.
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4
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Gantz VM, Bier E. Active genetics comes alive: Exploring the broad applications of CRISPR-based selfish genetic elements (or gene-drives): Exploring the broad applications of CRISPR-based selfish genetic elements (or gene-drives). Bioessays 2022; 44:e2100279. [PMID: 35686327 PMCID: PMC9397133 DOI: 10.1002/bies.202100279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/11/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based "active genetic" elements developed in 2015 bypassed the fundamental rules of traditional genetics. Inherited in a super-Mendelian fashion, such selfish genetic entities offered a variety of potential applications including: gene-drives to disseminate gene cassettes carrying desired traits throughout insect populations to control disease vectors or pest species, allelic drives biasing inheritance of preferred allelic variants, neutralizing genetic elements to delete and replace or to halt the spread of gene-drives, split-drives with the core constituent Cas9 endonuclease and guide RNA (gRNA) components inserted at separate genomic locations to accelerate assembly of complex arrays of genetic traits or to gain genetic entry into novel organisms (vertebrates, plants, bacteria), and interhomolog based copying systems in somatic cells to develop tools for treating inherited or infectious diseases. Here, we summarize the substantial advances that have been made on all of these fronts and look forward to the next phase of this rapidly expanding and impactful field.
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Affiliation(s)
- Valentino M Gantz
- Department of Cell and Developmental Biology, University of California, La Jolla, California, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, La Jolla, California, USA
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5
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A nickase Cas9 gene-drive system promotes super-Mendelian inheritance in Drosophila. Cell Rep 2022; 39:110843. [PMID: 35613590 PMCID: PMC9190248 DOI: 10.1016/j.celrep.2022.110843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/07/2022] [Accepted: 04/28/2022] [Indexed: 01/01/2023] Open
Abstract
CRISPR-based gene-drives have been proposed for managing insect populations, including disease-transmitting mosquitoes, due to their ability to bias their inheritance toward super-Mendelian rates (>50%). Current technologies use a Cas9 that introduces DNA double-strand breaks into the opposing wild-type allele to replace it with a copy of the gene-drive allele via DNA homology-directed repair. However, the use of different Cas9 versions is unexplored, and alternative approaches could increase the available toolkit for gene-drive designs. Here, we report a gene-drive that relies on Cas9 nickases that generate staggered paired nicks in DNA to propagate the engineered gene-drive cassette. We show that generating 5′ overhangs in the system yields efficient allelic conversion. The nickase gene-drive arrangement produces large, stereotyped deletions that are advantageous to eliminate viable animals carrying small mutations when targeting essential genes. Our nickase approach should expand the repertoire for gene-drive arrangements aimed at applications in mosquitoes and beyond. Gene-drives using wild-type Cas9 offer solutions to fight vector-borne diseases, yet alternative strategies are needed to increase the available toolkit. López Del Amo et al. describe a nickase-based gene-drive system that promotes super-Mendelian inheritance of an engineered cassette in the Drosophila germ line, providing alternative designs for CRISPR-based gene-drive.
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6
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Bharathkumar N, Sunil A, Meera P, Aksah S, Kannan M, Saravanan KM, Anand T. CRISPR/Cas-Based Modifications for Therapeutic Applications: A Review. Mol Biotechnol 2022; 64:355-372. [PMID: 34741732 PMCID: PMC8571677 DOI: 10.1007/s12033-021-00422-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022]
Abstract
The CRISPR-Cas genome editing system is an intrinsic property of a bacteria-based immune system. This employs a guide RNA to detect and cleave the PAM-associated target DNA or RNA in subsequent infections, by the invasion of a similar bacteriophage. The discovery of Cas systems has paved the way to overcome the limitations of existing genome editing tools. In this review, we focus on Cas proteins that are available for gene modifications among which Cas9, Cas12a, and Cas13 have been widely used in the areas of medicine, research, and diagnostics. Since CRISPR has been already proven for its potential research applications, the next milestone for CRISPR will be proving its efficacy and safety. In this connection, we systematically review recent advances in exploring multiple variants of Cas proteins and their modifications for therapeutic applications.
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Affiliation(s)
| | - Abraham Sunil
- Department of Animal Behavior and Physiology, Madurai Kamaraj University, Madurai, Tamil Nadu India
| | - Prabhakar Meera
- B Aatral Biosciences Private Limited, Bangalore, Karnataka India
| | - Sam Aksah
- B Aatral Biosciences Private Limited, Bangalore, Karnataka India
| | - Muthu Kannan
- B Aatral Biosciences Private Limited, Bangalore, Karnataka India
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7
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Verkuijl SAN, Ang JXD, Alphey L, Bonsall MB, Anderson MAE. The Challenges in Developing Efficient and Robust Synthetic Homing Endonuclease Gene Drives. Front Bioeng Biotechnol 2022; 10:856981. [PMID: 35419354 PMCID: PMC8996256 DOI: 10.3389/fbioe.2022.856981] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Making discrete and precise genetic changes to wild populations has been proposed as a means of addressing some of the world's most pressing ecological and public health challenges caused by insect pests. Technologies that would allow this, such as synthetic gene drives, have been under development for many decades. Recently, a new generation of programmable nucleases has dramatically accelerated technological development. CRISPR-Cas9 has improved the efficiency of genetic engineering and has been used as the principal effector nuclease in different gene drive inheritance biasing mechanisms. Of these nuclease-based gene drives, homing endonuclease gene drives have been the subject of the bulk of research efforts (particularly in insects), with many different iterations having been developed upon similar core designs. We chart the history of homing gene drive development, highlighting the emergence of challenges such as unintended repair outcomes, "leaky" expression, and parental deposition. We conclude by discussing the progress made in developing strategies to increase the efficiency of homing endonuclease gene drives and mitigate or prevent unintended outcomes.
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Affiliation(s)
- Sebald A. N. Verkuijl
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Joshua X. D. Ang
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
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8
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Kaduskar B, Kushwah RBS, Auradkar A, Guichard A, Li M, Bennett JB, Julio AHF, Marshall JM, Montell C, Bier E. Reversing insecticide resistance with allelic-drive in Drosophila melanogaster. Nat Commun 2022; 13:291. [PMID: 35022402 PMCID: PMC8755802 DOI: 10.1038/s41467-021-27654-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/02/2021] [Indexed: 12/27/2022] Open
Abstract
A recurring target-site mutation identified in various pests and disease vectors alters the voltage gated sodium channel (vgsc) gene (often referred to as knockdown resistance or kdr) to confer resistance to commonly used insecticides, pyrethroids and DDT. The ubiquity of kdr mutations poses a major global threat to the continued use of insecticides as a means for vector control. In this study, we generate common kdr mutations in isogenic laboratory Drosophila strains using CRISPR/Cas9 editing. We identify differential sensitivities to permethrin and DDT versus deltamethrin among these mutants as well as contrasting physiological consequences of two different kdr mutations. Importantly, we apply a CRISPR-based allelic-drive to replace a resistant kdr mutation with a susceptible wild-type counterpart in population cages. This successful proof-of-principle opens-up numerous possibilities including targeted reversion of insecticide-resistant populations to a native susceptible state or replacement of malaria transmitting mosquitoes with those bearing naturally occurring parasite resistant alleles. Insecticide resistance (IR) poses a major global health challenge. Here, the authors generate common IR mutations in laboratory Drosophila strains and use a CRISPR-based allelic-drive to replace an IR allele with a susceptible wild-type counterpart, providing a potent new tool for vector control.
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Affiliation(s)
- Bhagyashree Kaduskar
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India.,Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Raja Babu Singh Kushwah
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India.,Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Annabel Guichard
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Menglin Li
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Jared B Bennett
- Biophysics Graduate Group, Division of Biological Sciences, College of Letters and Science, University of California, Berkeley, CA, 94720, USA
| | | | - John M Marshall
- Division of Biostatistics and Epidemiology - School of Public Health, University of California, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Craig Montell
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA. .,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA.
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9
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Abstract
Gene drives are selfish genetic elements that are transmitted to progeny at super-Mendelian (>50%) frequencies. Recently developed CRISPR-Cas9-based gene-drive systems are highly efficient in laboratory settings, offering the potential to reduce the prevalence of vector-borne diseases, crop pests and non-native invasive species. However, concerns have been raised regarding the potential unintended impacts of gene-drive systems. This Review summarizes the phenomenal progress in this field, focusing on optimal design features for full-drive elements (drives with linked Cas9 and guide RNA components) that either suppress target mosquito populations or modify them to prevent pathogen transmission, allelic drives for updating genetic elements, mitigating strategies including trans-complementing split-drives and genetic neutralizing elements, and the adaptation of drive technology to other organisms. These scientific advances, combined with ethical and social considerations, will facilitate the transparent and responsible advancement of these technologies towards field implementation.
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Affiliation(s)
- Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA.
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10
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Grunwald HA, Weitzel AJ, Cooper KL. Applications of and considerations for using CRISPR-Cas9-mediated gene conversion systems in rodents. Nat Protoc 2022; 17:3-14. [PMID: 34949863 DOI: 10.1038/s41596-021-00646-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/13/2021] [Indexed: 01/23/2023]
Abstract
Genetic elements that are inherited at super-Mendelian frequencies could be used in a 'gene drive' to spread an allele to high prevalence in a population with the goal of eliminating invasive species or disease vectors. We recently demonstrated that the gene conversion mechanism underlying a CRISPR-Cas9-mediated gene drive is feasible in mice. Although substantial technical hurdles remain, overcoming these could lead to strategies that might decrease the spread of rodent-borne Lyme disease or eliminate invasive populations of mice and rats that devastate island ecology. Perhaps more immediately achievable at moderate gene conversion efficiency, applications in a laboratory setting could produce complex genotypes that reduce the time and cost in both dollars and animal lives compared with Mendelian inheritance strategies. Here, we discuss what we have learned from early efforts to achieve CRISPR-Cas9-mediated gene conversion, potential for broader applications in the laboratory, current limitations, and plans for optimizing this potentially powerful technology.
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Affiliation(s)
- Hannah A Grunwald
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Alexander J Weitzel
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
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11
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Bier E, Nizet V. Driving to Safety: CRISPR-Based Genetic Approaches to Reducing Antibiotic Resistance. Trends Genet 2021; 37:745-757. [PMID: 33745750 DOI: 10.1016/j.tig.2021.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Bacterial resistance to antibiotics has reached critical levels, skyrocketing in hospitals and the environment and posing a major threat to global public health. The complex and challenging problem of reducing antibiotic resistance (AR) requires a network of both societal and science-based solutions to preserve the most lifesaving pharmaceutical intervention known to medicine. In addition to developing new classes of antibiotics, it is essential to safeguard the clinical efficacy of existing drugs. In this review, we examine the potential application of novel CRISPR-based genetic approaches to reducing AR in both environmental and clinical settings and prolonging the utility of vital antibiotics.
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Affiliation(s)
- Ethan Bier
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA.
| | - Victor Nizet
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Collaborative to Halt Antibiotic-Resistant Microbes, Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA; Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA
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12
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Feng X, López Del Amo V, Mameli E, Lee M, Bishop AL, Perrimon N, Gantz VM. Optimized CRISPR tools and site-directed transgenesis towards gene drive development in Culex quinquefasciatus mosquitoes. Nat Commun 2021; 12:2960. [PMID: 34017003 PMCID: PMC8137705 DOI: 10.1038/s41467-021-23239-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
Culex mosquitoes are a global vector for multiple human and animal diseases, including West Nile virus, lymphatic filariasis, and avian malaria, posing a constant threat to public health, livestock, companion animals, and endangered birds. While rising insecticide resistance has threatened the control of Culex mosquitoes, advances in CRISPR genome-editing tools have fostered the development of alternative genetic strategies such as gene drive systems to fight disease vectors. However, though gene-drive technology has quickly progressed in other mosquitoes, advances have been lacking in Culex. Here, we develop a Culex-specific Cas9/gRNA expression toolkit and use site-directed homology-based transgenesis to generate and validate a Culex quinquefasciatus Cas9-expressing line. We show that gRNA scaffold variants improve transgenesis efficiency in both Culex quinquefasciatus and Drosophila melanogaster and boost gene-drive performance in the fruit fly. These findings support future technology development to control Culex mosquitoes and provide valuable insight for improving these tools in other species.
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Affiliation(s)
- Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Víctor López Del Amo
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Enzo Mameli
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, School of Medicine, Boston, MA, USA
| | - Megan Lee
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Alena L Bishop
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- HHMI, Harvard Medical School, Boston, MA, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
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13
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Li Z, Marcel N, Devkota S, Auradkar A, Hedrick SM, Gantz VM, Bier E. CopyCatchers are versatile active genetic elements that detect and quantify inter-homolog somatic gene conversion. Nat Commun 2021; 12:2625. [PMID: 33976171 PMCID: PMC8113449 DOI: 10.1038/s41467-021-22927-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/01/2021] [Indexed: 11/08/2022] Open
Abstract
CRISPR-based active genetic elements, or gene-drives, copied via homology-directed repair (HDR) in the germline, are transmitted to progeny at super-Mendelian frequencies. Active genetic elements also can generate widespread somatic mutations, but the genetic basis for such phenotypes remains uncertain. It is generally assumed that such somatic mutations are generated by non-homologous end-joining (NHEJ), the predominant double stranded break repair pathway active in somatic cells. Here, we develop CopyCatcher systems in Drosophila to detect and quantify somatic gene conversion (SGC) events. CopyCatchers inserted into two independent genetic loci reveal unexpectedly high rates of SGC in the Drosophila eye and thoracic epidermis. Focused RNAi-based genetic screens identify several unanticipated loci altering SGC efficiency, one of which (c-MYC), when downregulated, promotes SGC mediated by both plasmid and homologous chromosome-templates in human HEK293T cells. Collectively, these studies suggest that CopyCatchers can serve as effective discovery platforms to inform potential gene therapy strategies.
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Affiliation(s)
- Zhiqian Li
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Nimi Marcel
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Stephen M Hedrick
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA, USA.
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14
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López Del Amo V, Leger BS, Cox KJ, Gill S, Bishop AL, Scanlon GD, Walker JA, Gantz VM, Choudhary A. Small-Molecule Control of Super-Mendelian Inheritance in Gene Drives. Cell Rep 2021; 31:107841. [PMID: 32610142 PMCID: PMC7587219 DOI: 10.1016/j.celrep.2020.107841] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/20/2020] [Accepted: 06/09/2020] [Indexed: 11/29/2022] Open
Abstract
Synthetic CRISPR-based gene-drive systems have tremendous potential in public health and agriculture, such as for fighting vector-borne diseases or suppressing crop pest populations. These elements can rapidly spread in a population by breaching the inheritance limit of 50% dictated by Mendel's law of gene segregation, making them a promising tool for population engineering. However, current technologies lack control over their propagation capacity, and there are important concerns about potential unchecked spreading. Here, we describe a gene-drive system in Drosophila that generates an analog inheritance output that can be tightly and conditionally controlled to between 50% and 100%. This technology uses a modified SpCas9 that responds to a synthetic, orally available small molecule, fine-tuning the inheritance probability. This system opens a new avenue to feasibility studies for spatial and temporal control of gene drives using small molecules.
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Affiliation(s)
- Víctor López Del Amo
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Brittany S Leger
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kurt J Cox
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Shubhroz Gill
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alena L Bishop
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Garrett D Scanlon
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - James A Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA.
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15
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Xu XRS, Bulger EA, Gantz VM, Klanseck C, Heimler SR, Auradkar A, Bennett JB, Miller LA, Leahy S, Juste SS, Buchman A, Akbari OS, Marshall JM, Bier E. Active Genetic Neutralizing Elements for Halting or Deleting Gene Drives. Mol Cell 2020; 80:246-262.e4. [PMID: 32949493 PMCID: PMC10962758 DOI: 10.1016/j.molcel.2020.09.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 05/03/2020] [Accepted: 09/01/2020] [Indexed: 01/02/2023]
Abstract
CRISPR-Cas9-based gene drive systems possess the inherent capacity to spread progressively throughout target populations. Here we describe two self-copying (or active) guide RNA-only genetic elements, called e-CHACRs and ERACRs. These elements use Cas9 produced in trans by a gene drive either to inactivate the cas9 transgene (e-CHACRs) or to delete and replace the gene drive (ERACRs). e-CHACRs can be inserted at various genomic locations and carry two or more gRNAs, the first copying the e-CHACR and the second mutating and inactivating the cas9 transgene. Alternatively, ERACRs are inserted at the same genomic location as a gene drive, carrying two gRNAs that cut on either side of the gene drive to excise it. e-CHACRs efficiently inactivate Cas9 and can drive to completion in cage experiments. Similarly, ERACRs, particularly those carrying a recoded cDNA-restoring endogenous gene activity, can drive reliably to fully replace a gene drive. We compare the strengths of these two systems.
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Affiliation(s)
- Xiang-Ru Shannon Xu
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Emily A Bulger
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, and Gladstone Institutes, San Francisco, CA, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Carissa Klanseck
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Stephanie R Heimler
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Jared B Bennett
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lauren Ashley Miller
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Sarah Leahy
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Sara Sanz Juste
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Anna Buchman
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Omar S Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, Berkeley, CA, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA.
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16
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Nefedova LN. Drosophila melanogaster as a Model of Developmental Genetics: Modern Approaches and Prospects. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360420040050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Smith SJ, Davidson LA, Rebeiz M. Evolutionary expansion of apical extracellular matrix is required for the elongation of cells in a novel structure. eLife 2020; 9:55965. [PMID: 32338602 PMCID: PMC7266619 DOI: 10.7554/elife.55965] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
One of the fundamental gaps in our knowledge of how novel anatomical structures evolve is understanding the origins of the morphogenetic processes that form these features. Here, we traced the cellular development of a recently evolved morphological novelty, the posterior lobe of D. melanogaster. We found that this genital outgrowth forms through extreme increases in epithelial cell height. By examining the apical extracellular matrix (aECM), we also uncovered a vast matrix associated with the developing genitalia of lobed and non-lobed species. Expression of the aECM protein Dumpy is spatially expanded in lobe-forming species, connecting the posterior lobe to the ancestrally derived aECM network. Further analysis demonstrated that Dumpy attachments are necessary for cell height increases during posterior lobe development. We propose that the aECM presents a rich reservoir for generating morphological novelty and highlights a yet unseen role for aECM in regulating extreme cell height.
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Affiliation(s)
- Sarah Jacquelyn Smith
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Lance A Davidson
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, United States
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
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18
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Tomoyasu Y, Halfon MS. How to study enhancers in non-traditional insect models. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb212241. [PMID: 32034049 DOI: 10.1242/jeb.212241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcriptional enhancers are central to the function and evolution of genes and gene regulation. At the organismal level, enhancers play a crucial role in coordinating tissue- and context-dependent gene expression. At the population level, changes in enhancers are thought to be a major driving force that facilitates evolution of diverse traits. An amazing array of diverse traits seen in insect morphology, physiology and behavior has been the subject of research for centuries. Although enhancer studies in insects outside of Drosophila have been limited, recent advances in functional genomic approaches have begun to make such studies possible in an increasing selection of insect species. Here, instead of comprehensively reviewing currently available technologies for enhancer studies in established model organisms such as Drosophila, we focus on a subset of computational and experimental approaches that are likely applicable to non-Drosophila insects, and discuss the pros and cons of each approach. We discuss the importance of validating enhancer function and evaluate several possible validation methods, such as reporter assays and genome editing. Key points and potential pitfalls when establishing a reporter assay system in non-traditional insect models are also discussed. We close with a discussion of how to advance enhancer studies in insects, both by improving computational approaches and by expanding the genetic toolbox in various insects. Through these discussions, this Review provides a conceptual framework for studying the function and evolution of enhancers in non-traditional insect models.
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Affiliation(s)
| | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
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19
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López Del Amo V, Bishop AL, Sánchez C HM, Bennett JB, Feng X, Marshall JM, Bier E, Gantz VM. A transcomplementing gene drive provides a flexible platform for laboratory investigation and potential field deployment. Nat Commun 2020; 11:352. [PMID: 31953404 PMCID: PMC6969112 DOI: 10.1038/s41467-019-13977-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
CRISPR-based gene drives can spread through wild populations by biasing their own transmission above the 50% value predicted by Mendelian inheritance. These technologies offer population-engineering solutions for combating vector-borne diseases, managing crop pests, and supporting ecosystem conservation efforts. Current technologies raise safety concerns for unintended gene propagation. Herein, we address such concerns by splitting the drive components, Cas9 and gRNAs, into separate alleles to form a trans-complementing split-gene-drive (tGD) and demonstrate its ability to promote super-Mendelian inheritance of the separate transgenes. This dual-component configuration allows for combinatorial transgene optimization and increases safety by restricting escape concerns to experimentation windows. We employ the tGD and a small-molecule-controlled version to investigate the biology of component inheritance and resistant allele formation, and to study the effects of maternal inheritance and impaired homology on efficiency. Lastly, mathematical modeling of tGD spread within populations reveals potential advantages for improving current gene-drive technologies for field population modification.
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Affiliation(s)
- Víctor López Del Amo
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alena L Bishop
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Héctor M Sánchez C
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Jared B Bennett
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720, USA
| | - Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0349, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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20
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Guichard A, Haque T, Bobik M, Xu XRS, Klanseck C, Kushwah RBS, Berni M, Kaduskar B, Gantz VM, Bier E. Efficient allelic-drive in Drosophila. Nat Commun 2019; 10:1640. [PMID: 30967548 PMCID: PMC6456580 DOI: 10.1038/s41467-019-09694-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/21/2019] [Indexed: 01/08/2023] Open
Abstract
Gene-drive systems developed in several organisms result in super-Mendelian inheritance of transgenic insertions. Here, we generalize this "active genetic" approach to preferentially transmit allelic variants (allelic-drive) resulting from only a single or a few nucleotide alterations. We test two configurations for allelic-drive: one, copy-cutting, in which a non-preferred allele is selectively targeted for Cas9/guide RNA (gRNA) cleavage, and a more general approach, copy-grafting, that permits selective inheritance of a desired allele located in close proximity to the gRNA cut site. We also characterize a phenomenon we refer to as lethal-mosaicism that dominantly eliminates NHEJ-induced mutations and favors inheritance of functional cleavage-resistant alleles. These two efficient allelic-drive methods, enhanced by lethal mosaicism and a trans-generational drive process we refer to as "shadow-drive", have broad practical applications in improving health and agriculture and greatly extend the active genetics toolbox.
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Affiliation(s)
- Annabel Guichard
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Tisha Haque
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Marketta Bobik
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Xiang-Ru S Xu
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Carissa Klanseck
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Raja Babu Singh Kushwah
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society-India (TIGS), TIGS Center at inStem, Bangalore, 560065, India
| | - Mateus Berni
- Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Ilha do Fundão, Rio de Janeiro, 21941-902, RJ, Brazil
- Post-graduate Program in Morphological Sciences, Federal University of Rio de Janeiro (PCM/UFRJ), Rio de Janeiro, 21941-902, RJ, Brazil
| | - Bhagyashree Kaduskar
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society-India (TIGS), TIGS Center at inStem, Bangalore, 560065, India
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA.
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA, 92093-0335, USA.
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21
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Grunwald HA, Gantz VM, Poplawski G, Xu XRS, Bier E, Cooper KL. Super-Mendelian inheritance mediated by CRISPR-Cas9 in the female mouse germline. Nature 2019; 566:105-109. [PMID: 30675057 PMCID: PMC6367021 DOI: 10.1038/s41586-019-0875-2] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/07/2018] [Indexed: 01/02/2023]
Abstract
A gene drive biases the transmission of one of the two copies of a gene such that it is inherited more frequently than by random segregation. Highly efficient gene drive systems have recently been developed in insects, which leverage the sequence-targeted DNA cleavage activity of CRISPR-Cas9 and endogenous homology-directed repair mechanisms to convert heterozygous genotypes to homozygosity1-4. If implemented in laboratory rodents, similar systems would enable the rapid assembly of currently impractical genotypes that involve multiple homozygous genes (for example, to model multigenic human diseases). To our knowledge, however, such a system has not yet been demonstrated in mammals. Here we use an active genetic element that encodes a guide RNA, which is embedded in the mouse tyrosinase (Tyr) gene, to evaluate whether targeted gene conversion can occur when CRISPR-Cas9 is active in the early embryo or in the developing germline. Although Cas9 efficiently induces double-stranded DNA breaks in the early embryo and male germline, these breaks are not corrected by homology-directed repair. By contrast, Cas9 expression limited to the female germline induces double-stranded breaks that are corrected by homology-directed repair, which copies the active genetic element from the donor to the receiver chromosome and increases its rate of inheritance in the next generation. These results demonstrate the feasibility of CRISPR-Cas9-mediated systems that bias inheritance of desired alleles in mice and that have the potential to transform the use of rodent models in basic and biomedical research.
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Affiliation(s)
- Hannah A Grunwald
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Valentino M Gantz
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Gunnar Poplawski
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Xiang-Ru S Xu
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
| | - Ethan Bier
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, CA, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California, San Diego, La Jolla, CA, USA.
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA.
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22
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Guo Z, Qin J, Zhou X, Zhang Y. Insect Transcription Factors: A Landscape of Their Structures and Biological Functions in Drosophila and beyond. Int J Mol Sci 2018; 19:ijms19113691. [PMID: 30469390 PMCID: PMC6274879 DOI: 10.3390/ijms19113691] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 12/17/2022] Open
Abstract
Transcription factors (TFs) play essential roles in the transcriptional regulation of functional genes, and are involved in diverse physiological processes in living organisms. The fruit fly Drosophila melanogaster, a simple and easily manipulated organismal model, has been extensively applied to study the biological functions of TFs and their related transcriptional regulation mechanisms. It is noteworthy that with the development of genetic tools such as CRISPR/Cas9 and the next-generation genome sequencing techniques in recent years, identification and dissection the complex genetic regulatory networks of TFs have also made great progress in other insects beyond Drosophila. However, unfortunately, there is no comprehensive review that systematically summarizes the structures and biological functions of TFs in both model and non-model insects. Here, we spend extensive effort in collecting vast related studies, and attempt to provide an impartial overview of the progress of the structure and biological functions of current documented TFs in insects, as well as the classical and emerging research methods for studying their regulatory functions. Consequently, considering the importance of versatile TFs in orchestrating diverse insect physiological processes, this review will assist a growing number of entomologists to interrogate this understudied field, and to propel the progress of their contributions to pest control and even human health.
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Affiliation(s)
- Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianying Qin
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China.
| | - Xiaomao Zhou
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China.
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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23
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Gantz VM, Akbari OS. Gene editing technologies and applications for insects. CURRENT OPINION IN INSECT SCIENCE 2018; 28:66-72. [PMID: 30551769 PMCID: PMC6296244 DOI: 10.1016/j.cois.2018.05.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 05/09/2023]
Abstract
Initially discovered in bacteria, CRISPR-based genome editing endonucleases have proven remarkably amenable for adaptation to insects. To date, these endonucleases have been utilized in a plethora of both model and non-model insects including diverse flies, bees, beetles, butterflies, moths, and grasshoppers, to name a few, thereby revolutionizing functional genomics of insects. In addition to basic genome editing, they have also been invaluable for advanced genome engineering and synthetic biology applications. Here we explore the recent genome editing advancements in insects for generating site-specific genomic mutations, insertions, deletions, as well as more advanced applications such as Homology Assisted Genome Knock-in (HACK), potential to utilize DNA base editing, generating predictable reciprocal chromosomal translocations, and development gene drives to control the fate of wild populations.
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Affiliation(s)
- Valentino M Gantz
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92092, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92092, USA; Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, USA.
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